You mean the Engineers that had chemical weapons ready to attack Earth, and starting attacking the Prometheus crew without listening to any reason?

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I was just going to point that out. They were villians by any definition. As villians they weren't very well defined ones in terms of the over all plot and didn't have a lot of dialgoue but then again neither did the Xenomorphs.

Since we don't yet know why the Enginneers hate us, I'll call them probable villains. Many movie villains, notably Khan from STAR TREK INTO DARKNESS, are retaliating against co-villains or pseudo-villains. Possibly the final Enginner was doing so as well. We don't know yet. Boddicker, however, is pure uncut 107 precent ireedemo-but- hilarious villain.